DISCLAIMER: NCAR support for the Land Model Diagnostics
Package is limited to documentation found in this webpage. Land model analysis
requires an expert level of understanding of general circulation models, which
we cannot provide. These pages are intended to guide expert users only by
illustrating methods that have been successfully employed to further the
science of the Land Model Working Group.

1. Introduction: Lnd_diag v4.2

Background:

Lnd_diag4.2 was redesigned from earlier land diagnostic
packages (v2 and v3).Version 4 enables
paleo-climate reconstructions for all analyses.Version 4 produces bit-for-bit consistency with v2 and v3 and the
resulting analyses are identical. However, lnd_diag v4 run scripts are
not backward compatible with earlier versions.

1.a. Pre-processing Changes:

We
recommend that you pre-stage all the clm monthly history files before
running the LMWG diagnostics package.

The netCDF
Operators, or NCO, are a suite of programs known as operators. Each
operator is a standalone, command line program which is executed at the UNIX
shell-level. The operators take netCDF files as input,
then perform a set of operations (e.g., deriving new data, averaging,
hyperslabbing, or metadata manipulation) and produce a netCDF file as output.
The operators are primarily designed to aid manipulation and analysis of
gridded scientific data.

Swift is a scripting language for composing application programs into parallel applications that can be
executed on multicore processors, clusters, grids,
clouds, and supercomputers.

2. Run Script Documentation

NOTE: If you wish to stop
(i.e., kill) an analysis run during the pre-processing phase where the summary
files are being created you will need to first put the process into the
background:

Interrupt
the script by typing: cntrl^Z

Put
the process into the background by typing: ‘bg’

Get
the process ID by typing:‘jobs’

Kill
the process by typing: ‘ kill -9 %<process_id>’

Run Script Template:

Version

Run script template

Code source

lnd_diag4.2

lnd_template4.*.csh

CISL: /glade/p/cesm/lmwg/diag/lnd_diag4.2

CGD: /project/tss/diag/lnd_diag4.2

Section 1: Data Path

Environment Variable

Default Setting

Description

PTMPDIR

CISL: /glade/scratch/$LOGNAME

CGD: /scratch/$LOGNAME

Working directory

SOURCE_1

CISL: /glade/scratch/$LOGNAME

CGD: /scratch/$LOGNAME

File source 1

SOURCE_2

CISL: /glade/scratch/$LOGNAME

CGD: /scratch/$LOGNAME

File source 2

LOCAL_FLAG_1

0

look for history files in LOCAL_1

LOCAL_FLAG_2

0

look for history files in LOCAL_2

LOCAL_FLAG_atm_1

0

look for history files in LOCAL_1

LOCAL_FLAG_atm_2

0

look for history files in LOCAL_2

LOCAL_FLAG_rtm_1

0

look for history files in LOCAL_1

LOCAL_FLAG_rtm_2

0

look for history files in LOCAL_2

LOCAL_LN

1

1=create soft link; 0=copy files

Section 2: Source Path

NCAR users should
not need to change DIAG_HOME unless you wish to point to a local version of the
land diagnostics package (e.g., to make code modifications).Note that even if DIAG_HOME points to your
personal sandbox, OBS_HOME can still point to the default OBS_HOME directory to
save file space (the OBS_HOME directory is large).

Environment Variable

Default Setting

Description

DIAG_HOME

CISL: /glade/p/cesm/lmwg/diag/lnd_diag4.2

CGD: /project/tss/diag/lnd_diag4.2

maintained by LMWG maintained by LMWG

OBS_HOME

CISL: /glade/p/cesm/lmwg/diag/lnd_diag4.2

CGD: /project/tss/diag/lnd_diag4.2

maintained by LMWG maintained by LMWG

Section 3: Variable Lists

Do not change INPUT_HOME unless you wish to copy the
contents of this directory to a personal workspaceto create
non-standard variable lists for sets 1, 2 5, or 8. Note
that changing the variables analyzed in sets 3, 4, 6, and 7 requires
considerable code revision.

To create non-standard variable lists for sets 1, 2, 5, and
8:

·copy all variable lists from
$INPUT_HOME/inputFiles

·modify variable lists (original format is
required – Appendix A)

·Change INPUT_HOME to point to new variable
lists.

Environment Variable

Default Setting

Description

INPUT_HOME

/${DIAG_HOME}/lnd_diag4.2/code

Source lists maintained by LMWG

var_master_cn

Variable_master4.2.ncl

Current master variable list

Section 4: Type of Model Analysis

Environment Variable

Default Setting

Description

OBS

0

Model1 (vsObs
where avail)

ModelVsModel

1

Model1 vs Model 2 (vs Obs where avail)

Section 5: Run Identification

Environment
Variable

Default Setting

Description (0=ON;1=OFF)

prefix_1

clm3_6_14_newfrc_1995-2005

Name of output directory where analysis is
performed. The prefix name differentiates a particular diagnostic from
others within a series with the same case name. Convention uses the
analysis years to distinguish the run (e.g., clm3_6_14_newfrc_1948-2004)

caseid_1

clm3_6_14_newfrc

History file name (case1). This name identifies the
history files on the MSS

commonName_1

test

Descriptive name for plotting (optional)

UseCommonName_1

0

Use commonName for plots instead of caseid (optional).

prefix_2

clm4_1995-2005

output file and directory name (case2)

caseid_2

clm4

history file and MSS name (case2)

commonName_1

control

Descriptive name for plotting (optional) (case2)

UseCommonName_2

0

Use commonName for plots instead of caseid (optional).

Section 6a: MSS Paths

Environment
Variable

Default Setting

Description

MSS_tarfile_1

0

1=MSS annual tar files.

0=MSS monthly history files.

MSS_tarfile_2

0

1=MSS annual tar files.

0=MSS monthly history files.

MSS_path_1

/home/${USER}/csm/${caseid_1}/lnd/hist

Mass Storage System Path

MSS_path_2

/home/${USER}/csm/${caseid_2}/lnd/hist

Mass Storage System Path

MSS_path_atm_1

/home/${USER}/csm/${caseid_1}/atm/hist

Mass Storage System Path

MSS_path_atm_2

/home/${USER}/csm/${caseid_2}/atm/hist

Mass Storage System Path

MSS_path_rtm_1

/home/${USER}/csm/${caseid_1}/rof/hist

Mass Storage System Path

MSS_path_rtm_2

/home/${USER}/csm/${caseid_2}/rof/hist

Mass Storage System Path

Section 6b: Local Path

Environment
Variable

Default Setting

Description (0=ON; 1=OFF)

LOCAL_1

/glade/scratch/${USER}/${caseid_1}/lnd/hist.rename

Local file Path

LOCAL_2

/glade/scratch/${USER}/${caseid_2}/lnd/hist.rename

Local file Path

LOCAL_atm_1

/glade/scratch /${USER}/${caseid_1}/atm/hist

Local file Path

LOCAL_atm_2

/glade/scratch /${USER}/${caseid_2}/atm/hist

Local file Path

LOCAL_rtm_1

/glade/scratch /${USER}/${caseid_1}/rof/hist

Local file Path

LOCAL_rtm_2

/glade/scratch /${USER}/${caseid_2}/rof/hist

Local file Path

Section 6c: MSS storage path

Environment
Variable

Default Setting

Description

MSS_write

0

Write tar and summary files to MSS

MSS_pe

365

Retention period

MSS_proj

00000000

Project charged for MSS storage

Write2MSS_Only

0

Write MSS files ONLY (assumes processing is complete)

MSS_path_out1

/${UPPERCASE_USER}/csm/${caseid_1}/lnd/diag

MSS storage location for output

MSS_path_out2

/${UPPERCASE_USER}/csm/${caseid_2}/lnd/diag

MSS storage location for output

Section 7a: Summary File Processing

Post-process MSS files into summary files. This
section activates the post-processing of CCSM history files into the summary
files required by the diagnostics package. The diagnostics package will
fail if these files do not exist. Note that there is a significant
efficiency penalty for recreating the summary files if they already
exist. See Appendix for description of summary file requirements.

Environment Variable

Default Setting

Description

overWriteTrend

0

overwrite pre-existing trend files (ANN_ALL.nc)

overWriteClimo

0

overwrite pre-existing climo
files (DJF_climo.nc etc.)

weightAnnAvg

1

ON: Ann=(Jan*31+Feb*28+…+Dec*31)/365

OFF: Ann=(Jan
+Feb +…+Dec)/12

CASE 1

trends_1

1

construct long-term trends for case 1

climo_1

1

construct climatological means for case 1

trends_atm_1

0

construct long-term atmospheric trends for case 1

climo_atm_1

0

construct climatological atmospheric means for case 1

rtm_1

1

set to 1 if case 1 RTM files are on separate history files

trends_rtm_1

0

always set to 0 (no trends for RTM)

climo_rtm_1

1

construct climatological RTM
means for case 1

CASE 2

trends_2

1

construct long-term trends for case 2

climo_2

1

construct climatological means for case 2

trends_atm_2

0

construct long-term atmospheric trends for case 2

climo_atm_2

0

construct climatological atmospheric means for case 2

rtm_2

1

set to 1 if case 2 RTM files are on separate history files

trends_rtm_2

0

always set to 0 (no trends for RTM)

climo_rtm_2

1

construct climatological RTM
means for case 2

Section 7b: Seasonal Means Processing

Create seasonal means which are used for T-Test in set
2.

Environment Variable

Default Setting

Description

meansFlag

1

for OBS runs

meansFlag

1

Required for set 2 T-Test for ModelVsModel runs.

Section 8: Monthly, Seasonal and Annual Climatology.

Specify first year and number of years to be analyzed for
long-term climatologies. The ending year is calculated from clim_first_yr
+ clim_num_yrs. Model1 vs Model2 climatologies can compare different time
periods, but for consistency they should be averaged over the same number of
years.

Setting

Description

clim_first_yr_1

clim_first_yr_2

First model year for calculating model climatology.

clim_num_yrs_1

clim_num_yrs_2

Number of years to be included in climatology.

Example:

Environment Variable

Settings

clim_first_yr_1

1995

clim_num_yrs_1

11

clim_first_yr_2

1995

clim_num_yrs_1

11

Section 9: Annual trends.

User-specified first year and number of
years to be analyzed for long-term trends. The ending year is
calculated from trends_first_yr + trends_num_yrs. Model1 vs Model2 trends
can compare different time periods, and be of different lengths. For
comparisons between runs of different lengths and/or time periods, use Section 10
to indicate the first year of overlap for each case.

Setting

Description

trends_first_yr_1

trends_first_yr_2

First model year for calculating annual trends

trends_num_yrs_1

trends_num_yrs_2

Number of years to be included in annual trend analysis

Example:

Environment Variable

Settings

trends_first_yr_1

1995

trends_num_yrs_1

11

trends_first_yr_2

1995

trends_num_yrs_1

11

Section 10: Set Comparison Years (Optional)

Use this section to specify the first year of overlap
between cases 1 and 2 if the length and/or time periods differ between cases.

Environment Variable

Default Setting

Description

trends_match_Flag

0

1=Turn on overlapping time periods

trends_match_yr_1

1975

Identify first year of overlap for case 1

trends_match_yr_2

1995

Identify first year of overlap for case 2

Examples:

1) 100-179 vs 400-479

trends_match_Flag 1

trends_match_yr_1
100

trends_match_yr_2 400

Result: overlaps the two 80 yr periods

2) 100-179 vs 400-479

trends_match_Flag 1

trends_match_yr_1
170

trends_match_yr_2 400

Result: overlaps the last ten years of case 1 with the first 10
yrs of case 2.

3) 100-179 vs 100-179

trends_match_Flag 1

trends_match_yr_1
170

trends_match_yr_2 100

Result:
overlaps the last ten years of case 1 with the first 10 yrs of case 2.

4) 100-179 vs
100-179

trends_match_Flag 1

trends_match_yr_1
170

trends_match_yr_2 150

Result:
overlaps the last ten years of case 1 with the last 30 yrs of case 2.

Section 11: Optional Exit

Exit after reading MSS files and estimating trends and
climatologies.

Environment Variable

Default Setting

Description

Exit_after_MSS

0

Exit after downloading history files and calculating
trends and climotologies.

Section 12a: Carbon Models

Environment Variable

Default Setting

Description

CN

0

CN carbon model active

C13

0

C13 Isotopes active (INACTIVE)

CLAMP

0

CLAMP terminology (INACTIVE)

CASA

0

CASA terminology (INACTIVE)

Section 12b: Hydrology Variables

Environment Variable

Default Setting

Description

HYDRO

1

Hydrology plots active

Section 13: NaN Screening (Optional)

Pre-screen for NaNs in CCSM history files.
Script examines all variables in ANN_ALL.nc file for NaNs. User specifies
whether script allows NaNs and continues processing, or exits fatally if NaNs
are found. If BLOCK_NAN is set to 0 (thereby allowing the diagnostic
package to continue processing) all NaNs are set to missing in every set.
The goal of this step is to avoid potential problems by bring NaNs to the users
immediate attention, therefore the default/recommended settings enable both
set_0 and BLOCK_NAN.

Environment Variable

Default Setting

Description

set_0

1

Pre-screen for NaNs in derived files.

BLOCK_NAN

0

Exit script if NaNs are found.

Section 14: Analysis Sets

The diagnostics package performs a series of analyses that
are divided into sets for convenience. Setting the set to 1 activates
that analysis. Setting the set to 1 makes it inactive. See Appendix
for detailed description.

Section 15: Restart

This option is useful for runs that fail after
pre-processing, during the set analysis. For example: Sets 1, 2,
and 3 completed, but set 4 fails for an arbitrary external reason (e.g., the
machine goes down unexpectedly or you run out of space on your working
directory). To restart the run at set 4 and avoid re-running sets 1-3,
set the ‘restart_set_flag’ to 1, and set ‘restart_set’ to 4. Leave sets
1-3 turned on (1) so they are visible on the webpages where only active sets
are listed.

Environment Variable

Default Setting

Description

setRestart_flag

0

Turn on to restart analysis at ‘setRestart_set’.

setRestart_set

2

Valid options: 2,3,4,5,6,7,8,9

Section 16: User Preferences

Recommendation: New users should run a short test run
(e.g., 5 yrs) with these flags turned off to be sure the diagnostics packages
will run with their history files. Then turn the rmMonFiles* flags on to
remove history files and save file space for longer runs. If you plan to
extend this run by adding years or branching from the original diagnostics
(e.g., extending an initial analysis of years 1-40 to years 1-100), be sure
that deleteProcDir is turned off.

Environment Variable

Default Setting

Description

projection

0

1=Cylindrical Equidistant, 0=Robinson

colormap

1

1=use Blue-Yellow-Red, 0=use original colormaps

density

144

Controls density of output *.gif images

rmMonFilesTrend

0

Remove monthly history files after trends are created

rmMonFilesClimo

0

Remove monthly history files after climo files are created

raster

1

Raster mode for set 2 plots

expContours

0

All contours are user defined for set2 plots.To set explicit contours when
expContours=0, change 0 to 1 in $INPUT_HOME/set2_*.txt.

deleteProcDir

1

Delete processing directory

Section 17a: Web Pages

Environment Variable

Default setting

Description

web_pages

1

Create web page.

Section 17b: Processing directives

Environment Variable

Default

Setting

Description

delete_ps

1

Delete postscript files when analysis is complete.

delete_webdir

1

Delete web directory after tar file is created.

cleanup_Only

0

Cleanup directories after tar file is created (debug
option)

webpage_Only

0

Skip to webpage creation (debug option)

ps2gif_Only

0

Skip to ps2gif conversion (debug option)

convert

1

Convert from ps to gif (debug option)

Section 18: File Transfer

Send notification and scp tar file
to local machine where you would like to view results in a browser.

Environment Variable

Default

Setting

Description (1=ON; 0=OFF)

remote

1

Send email to user account

scpFile

0

Send tarfile to machine (requires interactive password)

Remote_system

‘mymachine’

Machine where you would like to post results.

Remote_dir

/web/web-date/tss/

Local directory where you would like to store results.

Email_address

‘myEmail@myaddress’

Your email address.

Section 19: Swift

For more details on using swift as part of the land
diagnostics package, see lnd_diag_swift4.2.XXXXXX.pdf in the top-level
directory (additional settings required). Currently the swift version is
supported only on the NWSC Geyser cluster.

“new” if NEE, NETRAD, LATENT, FSH are present in history
file, “old” otherwise

MODEL_TYPE2

“old”

“new” if NEE, NETRAD, LATENT, FSH are present in history
file, “old” otherwise

GRID_1

0.5

Model grid: 0.5, 0.9, 1.9, T31, or T42

GRID_2

0.5

Model grid: 0.5, 0.9, 1.9, T31, or T42

nlat_1

360

Number of latitudes on model1 grid

nlon_1

720

Number of longitudes on model1 grid

nlat_2

360

Number of latitudes on model2 grid

nlon_2

720

Number of longitudes on model2 grid

END Users Guide

Appendix

A1. Directory Tree – CCSM History Files

The directory tree is created
automatically by the land model diagnostics package (lnd_systems.csh). It
includes the case directory, the model run directory (working directory), and
subdirectories: model-obs or model1-model2.

PTMPDIR

case_1_dir

caseid_1_annT_YEAR.nc

caseid_1.clm2.h0.YEAR-MO.nc

caseid_2_annT_YEAR.nc

caseid_2.clm2.h0.YEAR-MO.nc

PTMPDIR

case_1_atm_dir

caseid_1_annT_atm_YEAR.nc

caseid_1.cam2.h0.YEAR_MO.nc

caseid_2_annT_atm_YEAR.nc

caseid_2.cam2.h0.YEAR-MO.nc

PTMPDIR

case_1_rtm_dir

caseid_1_annT_rtm_YEAR.nc

caseid_1.rtm.h0.YEAR_MO.nc

caseid_2_annT_rtm_YEAR.nc

caseid_2.rtm.h0.YEAR-MO.nc

A2. Directory Tree – Trend Files

PTMPDIR

prefix_1_dir

prefix_2_dir

prefix_1_ANN_ALL.nc

prefix_1_ANN_means.nc

prefix_2_ANN_ALL.nc

prefix_2_ANN_means.nc

PTMPDIR

prefix_1_atm_dir

prefix_2_atm_dir

prefix_1_ANN_ALL_atm.nc

prefix_1_ANN_means_atm.nc

prefix_2_ANN_ALL_atm.nc

prefix_2_ANN_means_atm.nc

PTMPDIR

prefix_1_rtm_dir

prefix_2_rtm_dir

prefix_1_ANN_means_rtm.nc

prefix_2_ANN_means_rtm.nc

A3: Directory Tree – Climatology Files

PTMPDIR

prefix_1_dir

prefix_2_dir

prefix_1_DJF_climo.nc

prefix_1_MAM_climo.nc

prefix_1_JJA_climo.nc
prefix_1_SON_climo.nc

prefix_1_MONS_climo.nc

prefix_1_ANN_climo.nc

prefix_2_DJF_climo.nc

prefix_2_MAM_climo.nc

prefix_2_JJA_climo.nc
prefix_2_SON_climo.nc

prefix_2_MONS_climo.nc

prefix_2_ANN_climo.nc

PTMPDIR

prefix_1_dir

prefix_2_dir

prefix_1_DJF_means.nc

prefix_1_MAM_means.nc

prefix_1_JJA_means.nc

prefix_1_SON_means.nc

prefix_1_ANN_climo.nc

prefix_1_ANN_means.nc

prefix_2_DJF_means.nc

prefix_2_MAM_means.nc

prefix_2_JJA_means.nc

prefix_2_SON_means.nc

prefix_2_ANN_climo.nc

prefix_2_ANN_means.nc

PTMPDIR

prefix_1_atm_dir

prefix_2_atm_dir

prefix_1_DJF_climo_atm.nc

prefix_1_MAM_climo_atm.nc

prefix_1_JJA_climo_atm.nc prefix_1_SON_climo_atm.nc

prefix_1_MONS_climo_atm.nc

prefix_1_ANN_climo_atm.nc

prefix_2_DJF_climo_atm.nc

prefix_2_MAM_climo_atm.nc

prefix_2_JJA_climo_atm.nc
prefix_2_SON_climo_atm.nc

prefix_2_MONS_climo_atm.nc

prefix_2_ANN_climo_atm.nc

PTMPDIR

prefix_1_atm_dir

prefix_2_atm_dir

prefix_1_DJF_means_atm.nc

prefix_1_MAM_means_atm.nc

prefix_1_JJA_means_atm.nc

prefix_1_SON_means_atm.nc

prefix_2_DJF_means_atm.nc

prefix_2_MAM_means_atm.nc

prefix_2_JJA_means_atm.nc

prefix_2_SON_means_atm.nc

PTMPDIR

prefix_1_rtm_dir

prefix_2_rtm_dir

prefix_1_DJF_climo_rtm.nc

prefix_1_MAM_climo_rtm.nc

prefix_1_JJA_climo_rtm.nc
prefix_1_SON_climo_rtm.nc

prefix_1_MONS_climo_rtm.nc

prefix_1_ANN_climo_rtm.nc

prefix_2_DJF_climo_rtm.nc

prefix_2_MAM_climo_rtm.nc

prefix_2_JJA_climo_rtm.nc
prefix_2_SON_climo_rtm.nc

prefix_2_MONS_climo_rtm.nc

prefix_2_ANN_climo_rtm.nc

PTMPDIR

prefix_1_rtm_dir

prefix_2_rtm_dir

prefix_1_DJF_means_rtm.nc

prefix_1_MAM_means_rtm.nc

prefix_1_JJA_means_rtm.nc

prefix_1_SON_means_rtm.nc

prefix_2_DJF_means_rtm.nc

prefix_2_MAM_means_rtm.nc

prefix_2_JJA_means_rtm.nc

prefix_2_SON_means_rtm.nc

A4: Directory Tree – Source Code

DIAG_HOME

code/shared

find_var_with_alts.ncl

functions_contrib.ncl

functions_tables.ncl

lnd_ann.pm

lnd_createTarFile.csh

lnd_create_webpage.pl

lnd_driver.csh

lnd_func.ncl

lnd_getFiles.pm

lnd_lookupTable.pl

lnd_mons.pm

lnd_NaNScreen.ncl

lnd_preProcDriver.pl

lnd_ps2gif.pl

lnd_regrid.pl

lnd_seas_climo.pm

lnd_seas_means.pm

lnd_statTable.pl

lnd_systems.csh

lnd_util.pm

lnd_varMaster.pl

lnd_write2mss.pl

mergeall.sh

plot_functions.ncl

raobs_station.ncl

read_obs.ncl

regional_values.ncl

regrid_history_ncl_wrapper.csh

regrid_history_standalone.pl

se2fv_esmf.genwgt.ncl

se2fv_esmf.regrid2file.ncl

DIAG_HOME

code/model-obs

set_1.ncl

set_2.ncl

set_3.ncl

set_4.ncl

set_5.ncl

set_6.ncl

set_7.ncl

set_8_DJF-JJA_contour.ncl

set_8_ann_cycle.ncl

set_8_ann_cycle_lnd.ncl

set_8_contour.ncl

set_8_trends.ncl

set_8_zonal.ncl

set_8_zonal_lnd.ncl

DIAG_HOME

code/model1-model2

set_1.ncl

set_1DiffPlot.ncl

set_2.ncl

set_3.ncl

set_4.ncl

set_5.ncl

set_6.ncl

set_7.ncl

set_8_DJF-JJA_contour.ncl

set_8_ann_cycle.ncl

set_8_ann_cycle_lnd.ncl

set_8_contour.ncl

set_8_trends.ncl

set_8_zonal.ncl

set_8_zonal_lnd.ncl

set_9.ncl

A5: Directory Tree – Swift Code

DIAG_HOME

swift/swift_configs/geyser

cf.properties

fs.data

sites.xml

tc.data

DIAG_HOME

swift/swift_utils

complete.csh

create_ANN_climo.pl

create_ANN_means.pl

createAnnualAll.pl

createAnnual.pl

create_MONS_climo_step2_1.pl

create_MONS_climo_step2_2.pl

create_MONS_climo_step2_3.pl

create_SEAS_climo_step1_1.pl

create_SEAS_climo_step1_2.pl

create_SEAS_climo_step2.pl

create_SEAS_means_step1.pl

create_SEAS_means_step2.pl

getDecFlag.csh

get_fileList.csh

lnd_ps2gif_swift.pl

lnd_util.pm

mergerCompareTable.csh

mfiles.csh

run_ncl_model_model.csh

run_ncl_model_obs.csh

run_pre-clamp_ncl.csh

run_clamp_ncl.csh

run_regridding.csh

A6: Directory Tree – CLAMP Code

DIAG_HOME

clamp/

00.initial.ncl

01.npp.ncl

02.lai.ncl

03.co2.ncl

04.biomass.ncl

06.fluxnet.ncl

07.beta.ncl

08.turnover.ncl

09.carbon_sink.ncl

09x.carbon_sink.ncl

10.fire.ncl

10.write_ameriflux_clm4.5BGC_RUN.ncl

11.ameriflux.ncl

20.write_fire_clm4.5BGC_RUN.ncl

99.final.ncl

README.old

run_1-model.csh

run_2-model.csh

taylor_diagram.ncl

test.csh

template_1-model/

template_1-model_noCO2/

template_2-model/

template_2-model_noCO2/

A7: Script Flags for Summary Files

_

Environment
Variable

Set

Description

trends_1

trends_2

Set 1

Set 6

Annual Trends

climo_1

climo_2

Set 2

Set 3

Set 5

Set 7

Monthly, annual and seasonal climatology and means

trends_atm_1

trends_atm_2

Set 8

Annual Trends (Atmosphere)

climo_atm_1

climo_atm_2

Set 4

Set 8

Monthly, annual and seasonal climatology and means
(Atmosphere)

trends_rtm_1

trends_rtm_2

Set 7

NA

climo_rtm_1

climo_rtm_2

Set 7

Monthly, annual and seasonal climatology and means (RTM)

A8: Set Description and Required Summary Files

Environment
Variable

Description

Temporal

Spatial

Required Summary
files

set_1

Line plots

Annual Trends

Global

ANN_ALL

set_2

Contour Plots

Long-term Climatology

Global

DJF_climo

MAM_climo

JJA_climo

SON_climo

DJF_means

MAM_ means

JJA_ means

SON_ means

set_3

Line plots

Monthly Climatology

Regional

region_definitions

MONS_climo

set_4

Vertical profiles of atmosphere

Long-term climatology

Global

RAOBS_new

ANN_climo_atm

MONS_climo_atm

set_5

Summary table by category and variable

Long-term climatology

Global

region_definitions

ANN_climo

set_6

Line plots

Annual Trends

Regional

region_definitions

ANN_ALL

set_7

River flow and discharge Note: the RTM output (QCHANR and
QCHOCNR) is at 0.5 degrees.

Long-term climatology

Regional and global

ANN_climo_rtm

MONS_climo_rtm

set_8 + set_8_lnd

Line and contour plots

OCN-ATMOS

tracers

Global

DJF_climo_atm

MAM_climo_atm

JJA_climo_atm

SON_climo_atm

MONS_climo_atm

ANN_ALL_atm

DJF_climo

MAM_climo

JJA_climo

SON_climo

set_9

Statistics table + contour plots

Monthly and seasonal climatology

Global

MONS_climo

DJF_climo

DJF_means

MAM_climo

MAM_means

JJA_climo

JJA_means

SON_climo

SON_means

A9: Summary File Creation

Summary file

Contents

Time

Dimension

Dimensions

Created by

annT

annT_atm

annT_rtm

Annual average from monthly history files. (ncra)

1

Time

Lat

Lon

lnd_util.pm

lnd_ann.pm

ANN_ALL

ANN_ALL_atm

Annual records for all years specified by trends_num_yrs,
starting with trends_first_yr.

nTrendYrs

Time

Lat

Lon

lnd_util.pm

lnd_ann.pm

ANN_climo

ANN_climo_atm

ANN_climo_rtm

Annual climatology

1

Time

Lat

Lon

lnd_ann.pm

MONS_climo

MONS_climo_atm

MONS_climo_rtm

Monthly Climatology

12 months

Time

Lat

Lon

lnd_mons.pm

DJF_climo

DJF_climo_atm

DJF_climo_rtm

MAM_climo

MAM_climo_atm

MAM_climo_rtm

JJA_climo

JJA_climo_atm

JJA_climo_rtm

SON_climo

SON_climo_atm

SON_climo_rtm

Seasonal Climatology

1

Time

Lat

Lon

lnd_seas_climo.pm

ANN_means

ANN_means_atm

ANN_means_rtm

Annual means

nClimYrs

Time

Lat

Lon

lnd_ann.pm

DJF_means

DJF_means_atm

DJF_means_rtm

MAM_ means

MAM_means_atm

MAM_means_rtm

JJA_means

JJA_means_atm

JJA_means_rtm

SON_means

SON_means_atm

SON_means_rtm

Seasonal means

nClimYrs

Time

Lat

Lon

lnd_util.pm

lnd_seas_means.pm

ANN_globalClimo

Global avg/total

nTrendYrs

time

Created by set_1.ncl from ANN_ALL.nc file

A10. Directory Tree – Input Files

DIAG_HOME

code/inputFiles

set1_c13.txt*

set1_clm.txt*

set1_cn.txt*

set2_c13.txt*

set2_clm.txt*

set2_cn.txt*

set3_cnFlx.txt*

set3_fireFlx.txt*

set3_landFlx.txt*

set3_moistEnergyFlx.txt*

set3_radFlx.txt*

set3_turbFlx.txt*

set4_stationIds.txt*

set5_c13.txt*

set5_clm.txt*

set5_cn.txt*

set5_hydReg.txt*

set6_cnFlx.txt*

set6_fireFlx.txt*

set6_landFlx.txt*

set6_radFlx.txt*

set6_turbFlx.txt*

set8_ann_cycle.txt*

set8_ann_cycle_lnd.txt*

set8_contour.txt*

set8_contour_DJF-JJA.txt*

set8_trends.txt*

set8_zonal.txt*

set8_zonal_lnd.txt*

variable_master4.2.ncl*

A11: Input File Format (Required)

Each set has a separate list of input files. The set
listing defines how the variables will be analyzed. For example, global
temperature is globally averaged, while annual GPP is represented as a global
total. In addition, sets may define the same variable differently
depending on the set. For example, set 1 treats NEE as an annual global sum, and as a global daily average for set 2.

Set 2 uses an additional column in the input files to
indicate whether the variable should be contoured using dynamic or pre-set
contour intervals. Pre-set contour intervals are defined in
variable_master4.2.ncl.

The addition of this feature allows the user to define the
contour intervals for selected variables without requiring that all variables
have either pre-set or dynamic contouring.

This feature is not available for set_8_contour.ncl,
therefore all contour levels for this set are dynamic.

A12: Required Input File format: Sets 1, 3, 4, 5, 6, 7, 8, 9

Format:

Column

1-6

7-10

11-13

14-16

17 –

Options

global

Mean

Totl

Day

Ann

Nat

[spaces]

Variable name from CCSM History file

Example:

globalTotlAnn
C13_NEE

globalTotlAnn
C13_NEP

globalTotlAnn
C13_GPP

globalTotlAnn C13_PSNSUN_TO_CPOOL

A13: Required Input File format: Set 2

Column

1-6

7-10

11-13

14

15-16

17 –

Options

global

Mean

Totl

Day

Ann

Nat

0

1

[spaces]

Variable name from CCSM History file

Example: Set 2

globalMeanDay0
NEE

globalMeanDay0
NEP

globalMeanDay0
GPP

globalMeanNat0
TSA

Options:

Columns 11-13:

Units

Ann

Annual units

Day

Daily units

Nat

Native units from history file

Column 14: Dynamic Contour flag (set 2 ONLY)

0

Dynamic contours

1

User defined contours

(NOTE: info@cn_Explicit must
also be True)

User-defined contour levels are
set in variable_master.ncl. If you define user-defined contours you
must copy the input files and variable_master to your personal workspace and
reset INPUT_HOME

Columns 17 - …

Variable Name

Variable must either be defined on the history file or
derived in lnd_func.ncl